I have two rather strange bugs here which I simply cant trace down.
First, because the stacktrace doesnt decode to anything useful, seems like its actually happening inside obfuscated SA code because the decoded stacktrace itself contains obfuscated calls seemingly outside our code.
Second, the exception thrown is in one case not throwable from anywhere in out code ( FormatException complaining about invalid Base64 chars ) and in the other case its explicitly catched yet is thrown and catched upwards only (IndexOutOfRangeException).

And, one of the bugs (FormatException) happens only when I use a debug executable with obfuscated release mode libraries. The other happens only in release/obfuscated mode.

I do have the slight feeling this might be an SA bug.

Any idea where to start searching? I can send the decoded stacktrace, maybe it decodes for you to something useful.

Which obfuscation mode are you using? (Is the decoding done using the direct stack decoding feature or through the exception reporting feature)? I think there are some issues with full decoding through the exception reporting feature but have not yet heard of any when using ASCII renaming.